The way I do imports from GIS:

1. I turn shapefiles into "spaghetti" osm files using a simplified version
of ogr2osm https://github.com/milovanderlinden/ogr2osm-light
2. Download osm data for the area your working in
3. Open the spaghetti files in josm, they will form seperate layers of ways
without any tags.
4. Manually work these extra layers through, clearing errors and adding tags
5. Select the objects from your layers you think are correct to be imported
in OSM and use Edit -> Merge selection (Ctrl+shift+m)
6. Upload to osm

I never do Merge layer as I think it is important to be able to manually
check for errors.

Maybe this is of some use to you.

Kind regards,

Milo van der Linden
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